[AMBER] tleap does not recognize nonstandard residue from lib file

From: JoAnne Babula <babula.ridgelinetherapeutics.com>
Date: Wed, 22 Jul 2020 14:43:59 -0500

Hello,

I am having problems when running the following tleap script to produce
topology and rst files for a complex (protein + small molecule [MAQ] +
co-factor [SAH]):







*source leaprc.protein.ff14SBsource leaprc.gaffloadamberparams
SAH.frcmodloadamberparams MAQ.frcmodloadoff SAH.libloadoff MAQ.libcomplex =
loadpdb X-hclean.pdb*

Resulting as follows:


































*Welcome to LEaP!(no leaprc in search path)Sourcing: ./complex.script-----
Source:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.protein.ff14SB-----
Source of
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.protein.ff14SB
doneLog file: ./leap.logLoading parameters:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/parm/parm10.datReading
title:PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNALoading
parameters:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/parm/frcmod.ff14SBReading
force field modification type file (frcmod)Reading title:ff14SB protein
backbone and sidechain parametersLoading library:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/lib/amino12.libLoading
library:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/lib/aminoct12.libLoading
library:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/lib/aminont12.lib-----
Source:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.gaff-----
Source of /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.gaff
doneLog file: ./leap.logLoading parameters:
/home1/apps/intel17/impi17_0/amber/16.0/dat/leap/parm/gaff.datReading
title:AMBER General Force Field for organic molecules (Version 1.8, Mar
2015)Loading parameters: ./SAH.frcmodReading force field modification type
file (frcmod)Reading title:remark goes hereLoading parameters:
./MAQ.frcmodReading force field modification type file (frcmod)Reading
title:remark goes hereLoading library: ./SAH.libLoading library:
./MAQ.libLoading PDB file: ./X-hclean.pdb*












































*-- residue 266: duplicate [ H2] atoms (total 2) Warning: Atom names in
each residue should be unique. (Same-name atoms are handled by using
the first occurrence and by ignoring the rest. Frequently
duplicate atom names stem from alternate conformations in the PDB
file.) Added missing heavy atom: .R<CLEU 264>.A<OXT 20>Created a new atom
named: N within residue: .R<SAH 266>Created a new atom named: CA within
residue: .R<SAH 266>Created a new atom named: CB within residue: .R<SAH
266>Created a new atom named: CG within residue: .R<SAH 266>Created a new
atom named: SD within residue: .R<SAH 266>Created a new atom named: C
within residue: .R<SAH 266>Created a new atom named: O within residue:
.R<SAH 266>Created a new atom named: OXT within residue: .R<SAH 266>Created
a new atom named: C5' within residue: .R<SAH 266>Created a new atom named:
C4' within residue: .R<SAH 266>Created a new atom named: O4' within
residue: .R<SAH 266>Created a new atom named: C3' within residue: .R<SAH
266>Created a new atom named: O3' within residue: .R<SAH 266>Created a new
atom named: C2' within residue: .R<SAH 266>Created a new atom named: O2'
within residue: .R<SAH 266>Created a new atom named: C1' within residue:
.R<SAH 266>Created a new atom named: N9 within residue: .R<SAH 266>Created
a new atom named: N7 within residue: .R<SAH 266>Created a new atom named:
HA within residue: .R<SAH 266>Created a new atom named: HB1 within residue:
.R<SAH 266>Created a new atom named: HB2 within residue: .R<SAH 266>Created
a new atom named: HG1 within residue: .R<SAH 266>Created a new atom named:
HG2 within residue: .R<SAH 266>Created a new atom named: H5'1 within
residue: .R<SAH 266>Created a new atom named: H5'2 within residue: .R<SAH
266>Created a new atom named: H4' within residue: .R<SAH 266>Created a new
atom named: H3' within residue: .R<SAH 266>Created a new atom named: HO3'
within residue: .R<SAH 266>Created a new atom named: H2' within residue:
.R<SAH 266>Created a new atom named: HO2' within residue: .R<SAH
266>Created a new atom named: H1' within residue: .R<SAH 266>Created a new
atom named: H61 within residue: .R<SAH 266>Created a new atom named: H62
within residue: .R<SAH 266> Added missing heavy atom: .R<SAH 266>.A<C13
24> Added missing heavy atom: .R<SAH 266>.A<C14 26>*




















* Added missing heavy atom: .R<SAH 266>.A<N5 23> Added missing heavy
atom: .R<SAH 266>.A<N2 17> Added missing heavy atom: .R<SAH 266>.A<C11
20> Added missing heavy atom: .R<SAH 266>.A<C12 21> Added missing heavy
atom: .R<SAH 266>.A<C9 16> Added missing heavy atom: .R<SAH 266>.A<C10
18> Added missing heavy atom: .R<SAH 266>.A<N4 22> Added missing heavy
atom: .R<SAH 266>.A<O3 11> Added missing heavy atom: .R<SAH 266>.A<C7 12>
Added missing heavy atom: .R<SAH 266>.A<O5 15> Added missing heavy atom:
.R<SAH 266>.A<O4 13> Added missing heavy atom: .R<SAH 266>.A<S1 5> Added
missing heavy atom: .R<SAH 266>.A<C3 4> Added missing heavy atom: .R<SAH
266>.A<C1 2> Added missing heavy atom: .R<SAH 266>.A<O1 7> Added missing
heavy atom: .R<SAH 266>.A<O2 8> total atoms in file: 4237 Leap added 36
missing atoms according to residue templates: 19 Heavy 17 H /
lone pairs The file contained 33 atoms not in residue templates*

I have already loaded the frcmod and mol2 files for the SAH non-standard
residue but it seems they were not recognized. Also, mol2 and frcmod for
SAH were generated using a Gaussian 16rA.03 rev A.03 output gesp file.
Please assist. The file contents are as follows:

SAH.mol2:
.<TRIPOS>MOLECULE
SAH
   46 48 1 0 0
SMALL
resp


.<TRIPOS>ATOM
      1 N1 4.7930 2.8050 -0.3140 n4 1 SAH
 -0.610549
      2 C1 4.9980 1.6710 0.6690 c3 1 SAH
0.063241
      3 C2 4.0070 0.5260 0.4660 c3 1 SAH
 -0.156260
      4 C3 4.2170 -0.2590 -0.8310 c3 1 SAH
0.279216
      5 S1 3.1240 -1.6960 -1.0460 ss 1 SAH
 -0.278619
      6 C4 6.5020 1.2580 0.4940 c 1 SAH
0.803463
      7 O1 7.1010 1.9630 -0.3360 o 1 SAH
 -0.741275
      8 O2 6.8500 0.3230 1.1790 o 1 SAH
 -0.741275
      9 C5 1.4950 -0.9300 -1.3280 c3 1 SAH
 -0.423766
     10 C6 0.6010 -0.9530 -0.0970 c3 1 SAH
0.326755
     11 O3 -0.5540 -0.1880 -0.3830 os 1 SAH
 -0.594334
     12 C7 0.0990 -2.3540 0.3260 c3 1 SAH
 -0.073682
     13 O4 0.2920 -2.5900 1.6960 oh 1 SAH
 -0.693896
     14 C8 -1.4140 -2.2620 0.0920 c3 1 SAH
0.164159
     15 O5 -2.1830 -3.0750 0.9010 oh 1 SAH
 -0.718555
     16 C9 -1.6580 -0.7610 0.2660 c3 1 SAH
0.578746
     17 N2 -2.8680 -0.2530 -0.3040 na 1 SAH
 -0.372947
     18 C10 -3.2990 -0.3410 -1.6080 cc 1 SAH
0.349863
     19 N3 -4.4060 0.2590 -1.8330 nd 1 SAH
 -0.638758
     20 C11 -4.7560 0.7980 -0.6080 ca 1 SAH
 -0.047356
     21 C12 -5.8470 1.5620 -0.1780 ca 1 SAH
0.819308
     22 N4 -6.8310 1.9500 -1.0090 nh 1 SAH
 -0.975473
     23 N5 -5.8960 1.9360 1.0950 nb 1 SAH
 -0.862961
     24 C13 -4.9060 1.5750 1.9030 ca 1 SAH
0.677210
     25 N6 -3.8370 0.8640 1.6200 nb 1 SAH
 -0.873988
     26 C14 -3.8110 0.4950 0.3450 ca 1 SAH
0.634084
     27 H1 4.1460 2.5970 -1.0550 hn 1 SAH
0.358704
     28 H2 4.5120 3.6690 0.1180 hn 1 SAH
0.358704
     29 H3 5.7630 2.8870 -0.6970 hn 1 SAH
0.358704
     30 H4 4.8670 2.0890 1.6570 hx 1 SAH
0.094068
     31 H5 2.9930 0.9120 0.5270 hc 1 SAH
0.076596
     32 H6 4.1480 -0.1450 1.3030 hc 1 SAH
0.076596
     33 H7 5.2160 -0.6750 -0.8440 h1 1 SAH
0.013433
     34 H8 4.1200 0.3650 -1.7150 h1 1 SAH
0.013433
     35 H9 1.0200 -1.4640 -2.1420 h1 1 SAH
0.176120
     36 H10 1.6290 0.0930 -1.6590 h1 1 SAH
0.176120
     37 H11 1.1150 -0.5100 0.7470 h1 1 SAH
0.062536
     38 H12 0.5500 -3.1500 -0.2530 h1 1 SAH
0.195993
     39 H13 1.1890 -2.8400 1.8740 ho 1 SAH
0.455561
     40 H14 -1.6310 -2.5310 -0.9340 h1 1 SAH
0.111402
     41 H15 -1.7680 -3.1600 1.7510 ho 1 SAH
0.489286
     42 H16 -1.6780 -0.4960 1.3140 h2 1 SAH
0.073568
     43 H17 -2.7290 -0.8640 -2.3480 h5 1 SAH
0.099654
     44 H18 -7.6470 2.3600 -0.6130 hn 1 SAH
0.428860
     45 H19 -6.8940 1.5480 -1.9160 hn 1 SAH
0.428860
     46 H20 -4.9990 1.9090 2.9200 h5 1 SAH
0.059450
.<TRIPOS>BOND
     1 1 2 1
     2 1 27 1
     3 1 28 1
     4 1 29 1
     5 2 3 1
     6 2 6 1
     7 2 30 1
     8 3 4 1
     9 3 31 1
    10 3 32 1
    11 4 5 1
    12 4 33 1
    13 4 34 1
    14 5 9 1
    15 6 7 1
    16 6 8 1
    17 9 10 1
    18 9 35 1
    19 9 36 1
    20 10 11 1
    21 10 12 1
    22 10 37 1
    23 11 16 1
    24 12 13 1
    25 12 14 1
    26 12 38 1
    27 13 39 1
    28 14 15 1
    29 14 16 1
    30 14 40 1
    31 15 41 1
    32 16 17 1
    33 16 42 1
    34 17 18 1
    35 17 26 1
    36 18 19 2
    37 18 43 1
    38 19 20 1
    39 20 21 ar
    40 20 26 ar
    41 21 22 1
    42 21 23 ar
    43 22 44 1
    44 22 45 1
    45 23 24 ar
    46 24 25 ar
    47 24 46 1
    48 25 26 ar
.<TRIPOS>SUBSTRUCTURE
     1 SAH 1 TEMP 0 **** **** 0 ROOT



SAH.frcmod:
remark goes here
MASS

BOND

ANGLE

DIHE

IMPROPER
c3-o -c -o 1.1 180.0 2.0 General
improper torsional angle (1 general atom type)
c3-ca-na-cc 1.1 180.0 2.0 Using default
value
h5-na-cc-nd 1.1 180.0 2.0 Using default
value
ca-ca-ca-nd 1.1 180.0 2.0 Using default
value
ca-nb-ca-nh 1.1 180.0 2.0 Using default
value
ca-hn-nh-hn 1.1 180.0 2.0 Using default
value
h5-nb-ca-nb 1.1 180.0 2.0 Using default
value
ca-na-ca-nb 1.1 180.0 2.0 Using default
value

NONBON

The pdb file "X-hclean.pdb" is attached. The portion encoding for SAH is as
follows:

HETATM 4193 N SAH 266 1.502 -2.774 -2.109 1.00 15.86
  N
HETATM 4194 CA SAH 266 2.813 -3.459 -2.517 1.00 15.86
  C
HETATM 4195 CB SAH 266 2.967 -3.475 -4.066 1.00 15.86
  C
HETATM 4196 CG SAH 266 3.245 -2.124 -4.758 1.00 15.86
  C
HETATM 4197 SD SAH 266 3.738 -2.253 -6.505 1.00 15.86
  S
HETATM 4198 C SAH 266 3.980 -2.781 -1.754 1.00 15.86
  C
HETATM 4199 O SAH 266 3.779 -1.802 -0.998 1.00 15.86
  O
HETATM 4200 OXT SAH 266 5.110 -3.273 -1.943 1.00 15.86
  O
HETATM 4201 C5' SAH 266 2.232 -1.756 -7.391 1.00 15.86
  C
HETATM 4202 C4' SAH 266 1.032 -2.680 -7.153 1.00 15.86
  C
HETATM 4203 O4' SAH 266 -0.104 -2.118 -7.800 1.00 15.86
  O
HETATM 4204 C3' SAH 266 1.197 -4.075 -7.780 1.00 15.86
  C
HETATM 4205 O3' SAH 266 0.904 -5.096 -6.853 1.00 15.86
  O
HETATM 4206 C2' SAH 266 0.302 -4.047 -9.018 1.00 15.86
  C
HETATM 4207 O2' SAH 266 -0.262 -5.278 -9.442 1.00 15.86
  O
HETATM 4208 C1' SAH 266 -0.773 -3.087 -8.539 1.00 15.86
  C
HETATM 4209 N9 SAH 266 -1.647 -2.446 -9.594 1.00 15.86
  N
HETATM 4210 C8 SAH 266 -1.348 -2.089 -10.860 1.00 15.86
  C
HETATM 4211 N7 SAH 266 -2.350 -1.548 -11.508 1.00 15.86
  N
HETATM 4212 C5 SAH 266 -3.347 -1.523 -10.609 1.00 15.86
  C
HETATM 4213 C6 SAH 266 -4.680 -1.064 -10.697 1.00 15.86
  C
HETATM 4214 N6 SAH 266 -5.223 -0.531 -11.864 1.00 15.86
  N
HETATM 4215 N1 SAH 266 -5.469 -1.165 -9.594 1.00 15.86
  N
HETATM 4216 C2 SAH 266 -4.943 -1.711 -8.489 1.00 15.86
  C
HETATM 4217 N3 SAH 266 -3.708 -2.192 -8.289 1.00 15.86
  N
HETATM 4218 C4 SAH 266 -2.943 -2.064 -9.401 1.00 15.86
  C
HETATM 4219 H1 SAH 266 0.725 -3.183 -2.611 1.00 0.00
  H
HETATM 4220 H2 SAH 266 1.343 -2.890 -1.118 1.00 0.00
  H
HETATM 4221 H3 SAH 266 1.538 -1.787 -2.326 1.00 0.00
  H
HETATM 4222 HA SAH 266 2.682 -4.361 -2.184 1.00 15.86
  H
HETATM 4223 HB1 SAH 266 2.174 -3.870 -4.460 1.00 15.86
  H
HETATM 4224 HB2 SAH 266 3.694 -4.076 -4.292 1.00 15.86
  H
HETATM 4225 HG1 SAH 266 3.986 -1.678 -4.319 1.00 15.86
  H
HETATM 4226 HG2 SAH 266 2.483 -1.531 -4.663 1.00 15.86
  H
HETATM 4227 H5'1 SAH 266 2.443 -1.720 -8.337 1.00 15.86
  H
HETATM 4228 H5'2 SAH 266 2.012 -0.851 -7.121 1.00 15.86
  H
HETATM 4229 H4' SAH 266 0.835 -2.716 -6.204 1.00 15.86
  H
HETATM 4230 H3' SAH 266 2.111 -4.222 -8.069 1.00 15.86
  H
HETATM 4231 HO3' SAH 266 0.109 -5.016 -6.594 1.00 15.86
  H
HETATM 4232 H2' SAH 266 0.781 -3.615 -9.743 1.00 15.86
  H
HETATM 4233 HO2' SAH 266 -0.601 -5.666 -8.778 1.00 15.86
  H
HETATM 4234 H1' SAH 266 -1.374 -3.545 -7.930 1.00 15.86
  H
HETATM 4235 H8 SAH 266 -0.462 -2.242 -11.225 1.00 15.86
  H
HETATM 4236 H61 SAH 266 -6.217 -0.350 -11.914 1.00 0.00
  H
HETATM 4237 H62 SAH 266 -4.648 -0.496 -12.693 1.00 0.00
  H
HETATM 4238 H2 SAH 266 -5.543 -1.783 -7.731 1.00 15.86
  H
END
-- 
Best regards,
JoAnne Babula, Ph.D.
Research Scientist
Ridgeline Therapeutics
2450 Holcombe Blvd, Suite J
Houston, TX 77021



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Received on Wed Jul 22 2020 - 13:00:06 PDT
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